Single nucleotide polymorphisms (SNPs) account for the majority of human genetic variability. Combination of common variants has been postulated to contribute significantly to genetic risk for common diseases, as well as having been implicated in more catastrophic health issues such as drug response. Additionally, SNPs can be used to study microbial pathogens. Thus there is great interest in small-scale SNP discovery projects directed at specific loci. SNP detection projects generate massive amounts of data, most of which is currently managed using laboratory notebooks and spreadsheets even though most of the data can be captured and managed automatically. The proposed protocol-specific information management system, tailored to SNP detection with specialized user input screen and analytic algorithms, will expedite the discovery of SNPs and accelerate knowledge acquisition.